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PDBsum entry 1vdd
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Recombination
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PDB id
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1vdd
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Contents |
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* Residue conservation analysis
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References listed in PDB file
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Key reference
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Title
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Ring-Shaped architecture of recr: implications for its role in homologous recombinational DNA repair.
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Authors
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B.I.Lee,
K.H.Kim,
S.J.Park,
S.H.Eom,
H.K.Song,
S.W.Suh.
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Ref.
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EMBO J, 2004,
23,
2029-2038.
[DOI no: ]
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PubMed id
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Abstract
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RecR, together with RecF and RecO, facilitates RecA loading in the RecF pathway
of homologous recombinational DNA repair in procaryotes. The human Rad52 protein
is a functional counterpart of RecFOR. We present here the crystal structure of
RecR from Deinococcus radiodurans (DR RecR). A monomer of DR RecR has a
two-domain structure: the N-terminal domain with a helix-hairpin-helix (HhH)
motif and the C-terminal domain with a Cys4 zinc-finger motif, a Toprim domain
and a Walker B motif. Four such monomers form a ring-shaped tetramer of 222
symmetry with a central hole of 30-35 angstroms diameter. In the crystal, two
tetramers are concatenated, implying that the RecR tetramer is capable of
opening and closing. We also show that DR RecR binds to both dsDNA and ssDNA,
and that its HhH motif is essential for DNA binding.
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Figure 3.
Figure 3 Detailed views of domains/motifs in DR RecR. (A) HhH
motifs from two monomers are swapped. Gly21, Arg23 and Lys27 are
shown. Primed residues belong to the second subunit B in Figure
2C. (B) Cys[4] zinc-finger motif. (C) Toprim domain with
residues Glu86, Asp90 and Glu146. Corresponding positions (142
and 144) of the 'DxD' sequence are indicated by red balls. (D)
The C-terminal regions from two monomers are swapped. Arg167 and
Asp182 are the fingerprint residues of the canonical Walker B
motif. Double-primed residues belong to the third subunit C. The
orientations of domains/motifs are roughly similar to those in
subunits B (colored in white green), D (purple) and C (white
blue) in Figure 2C.
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Figure 5.
Figure 5 A possible DNA clamp model for RecR. (A) Comparison of
DR RecR with DNA clamp proteins. Ribbon diagrams and
electrostatic potential at the molecular surface are shown for
DR RecR, E. coli DNA polymerase III  subunit,
T4 gp45 and human PCNA. The diameter of the central hole is
about 30 -35 Å for DR RecR and about 35 Å for other clamp
proteins. The molecular surface was colored according to the
electrostatic potential: blue, 10 kT; white, 0 kT; red, -10 kT.
(B) Conserved residues of DR RecR located in the putative
DNA-binding region of the central hole (left). Strictly
conserved residues are colored in green and semiconserved
residues in yellow, as deduced by aligning 14 RecR sequences in
Figure 1. Negatively charged residues of the Toprim domain and
the Walker B motif that may play a role in Mg2+-enhanced DNA
binding (right). (C) Model for dsDNA binding by DR RecR.
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The above figures are
reprinted
from an Open Access publication published by Macmillan Publishers Ltd:
EMBO J
(2004,
23,
2029-2038)
copyright 2004.
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